[med-svn] [snakemake] 03/04: Merge tag 'upstream/3.8.2+dfsg'

[Kevin Murray]

This is an automated email from the git hooks/post-receive script.

daube-guest pushed a commit to branch master
in repository snakemake.

commit 39f71be6526cb0e010295467cb3667944a610d71
Merge: b2416e5 1881744
Author: Kevin Murray <spam at kdmurray.id.au>
Date:   Sun Nov 13 22:04:15 2016 +1100

    Merge tag 'upstream/3.8.2+dfsg'
    
    Upstream version 3.8.2+dfsg

 .gitignore                                         |   1 +
 CHANGELOG.md                                       |  23 ++
 bitbucket-pipelines.yml                            |   9 +
 environment.yml                                    |   2 +
 setup.py                                           |  15 +-
 snakemake/__init__.py                              |  37 ++-
 snakemake/dag.py                                   | 138 ++++++----
 snakemake/executors.py                             | 108 ++++----
 snakemake/io.py                                    | 120 ++++++--
 snakemake/jobs.py                                  | 108 ++++++--
 snakemake/logging.py                               |  30 +-
 snakemake/parser.py                                |  25 +-
 snakemake/remote/FTP.py                            |  76 +++---
 snakemake/remote/SFTP.py                           |  18 +-
 snakemake/remote/__init__.py                       |  35 ++-
 snakemake/rules.py                                 | 304 ++++++++++++++-------
 snakemake/scheduler.py                             |  11 +-
 snakemake/script.py                                |  49 ++++
 snakemake/stats.py                                 |   2 +-
 snakemake/utils.py                                 | 107 ++++++--
 snakemake/version.py                               |   2 +-
 snakemake/workflow.py                              |  37 ++-
 tests/test_deferred_func_eval/Snakefile            |  22 ++
 .../expected-results/test.out                      |   1 +
 tests/test_deferred_func_eval/test1.in             |   0
 tests/test_deferred_func_eval/test2.in             |   0
 tests/test_delete_output/Snakefile                 |  23 ++
 .../expected-results/foo/output.foo.file           |   0
 .../expected-results/output.file                   |   0
 tests/test_format_params/Snakefile                 |   5 +
 tests/test_format_params/expected-results/test.out |   1 +
 tests/test_get_log_both/Snakefile                  |   6 +
 tests/test_get_log_both/expected-results/test.log  |   2 +
 tests/test_get_log_both/expected-results/test.out  |   2 +
 tests/test_get_log_both/test.in                    |   2 +
 tests/test_get_log_both/test.out                   |   2 +
 tests/test_get_log_both/wrapper.py                 |   7 +
 tests/test_get_log_complex/Snakefile               |   6 +
 .../test_get_log_complex/expected-results/test.log |   3 +
 .../test_get_log_complex/expected-results/test.out |   2 +
 tests/test_get_log_complex/test.in                 |   2 +
 tests/test_get_log_complex/test.out                |   2 +
 tests/test_get_log_complex/wrapper.py              |  11 +
 tests/test_get_log_none/Snakefile                  |   5 +
 tests/test_get_log_none/expected-results/test.out  |   2 +
 tests/test_get_log_none/test.in                    |   2 +
 tests/test_get_log_none/wrapper.py                 |   7 +
 tests/test_get_log_stderr/Snakefile                |   6 +
 .../test_get_log_stderr/expected-results/test.log  |   1 +
 .../test_get_log_stderr/expected-results/test.out  |   2 +
 tests/test_get_log_stderr/test.in                  |   2 +
 tests/test_get_log_stderr/test.out                 |   2 +
 tests/test_get_log_stderr/wrapper.py               |   7 +
 tests/test_get_log_stdout/Snakefile                |   6 +
 .../test_get_log_stdout/expected-results/test.log  |   1 +
 .../test_get_log_stdout/expected-results/test.out  |   2 +
 tests/test_get_log_stdout/test.in                  |   2 +
 tests/test_get_log_stdout/test.out                 |   2 +
 tests/test_get_log_stdout/wrapper.py               |   7 +
 tests/test_io.py                                   |  33 +++
 tests/test_issue328/Snakefile                      |  26 ++
 tests/test_issue328/expected-results/out.txt       |   0
 tests/test_issue328/in.txt                         |   0
 tests/test_remote_sftp/Snakefile                   |  10 +
 tests/test_remote_sftp/expected-results/readme.txt |  10 +
 tests/test_shadow/Snakefile                        |  68 ++++-
 tests/test_spaces_in_fnames/Snakefile              |  21 ++
 .../expected-results/test bam file realigned.bam   |   0
 tests/test_spaces_in_fnames/qsub                   |   6 +
 tests/test_spaces_in_fnames/test bam file.bam      |   0
 tests/test_static_remote/S3MockedForStaticTest.py  | 141 ++++++++++
 tests/test_static_remote/Snakefile                 |  42 +++
 tests/test_static_remote/__init__.py               |   0
 tests/test_static_remote/expected-results/out1.txt |   1 +
 tests/test_static_remote/expected-results/out2.txt |   1 +
 tests/test_static_remote/out1.txt                  |   1 +
 tests/test_static_remote/out2.txt                  |   1 +
 tests/test_static_remote/test.txt                  |   1 +
 tests/test_subworkflows/Snakefile                  |   1 +
 tests/test_subworkflows/subconfig.yaml             |   2 +
 tests/test_symlink_time_handling/Snakefile         |  68 +++++
 .../expected-results/time_diff.txt                 |   1 +
 tests/test_wildcard_keyword/Snakefile              |  35 +++
 .../expected-results/globalbar.log                 |   0
 .../expected-results/globalbar.txt                 |   1 +
 .../expected-results/localbar.log                  |   0
 .../expected-results/localbar.txt                  |   1 +
 .../expected-results/stringbar.log                 |   0
 .../expected-results/stringbar.txt                 |   1 +
 tests/tests.py                                     |  81 +++++-
 90 files changed, 1604 insertions(+), 361 deletions(-)

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